Automake uses these to determine which files to create (see Creating Output Files in The Autoconf Manual). A listed file
is considered to be an Automake generated Makefile if there
exists a file with the same name and the .am extension appended.
Typically, ‘AC_CONFIG_FILES([foo/Makefile])’ will cause Automake to
generate foo/Makefile.in if foo/Makefile.am exists.

When using AC_CONFIG_FILES with multiple input files, as in

AC_CONFIG_FILES([Makefile:top.in:Makefile.in:bot.in])

automake will generate the first .in input file for
which a .am file exists. If no such file exists the output
file is not considered to be generated by Automake.

Files created by AC_CONFIG_FILES, be they Automake
Makefiles or not, are all removed by ‘make distclean’.
Their inputs are automatically distributed, unless they
are the output of prior AC_CONFIG_FILES commands.
Finally, rebuild rules are generated in the Automake Makefile
existing in the subdirectory of the output file, if there is one, or
in the top-level Makefile otherwise.

The above machinery (cleaning, distributing, and rebuilding) works
fine if the AC_CONFIG_FILES specifications contain only
literals. If part of the specification uses shell variables,
automake will not be able to fulfill this setup, and you will
have to complete the missing bits by hand. For instance, on

file=input
…
AC_CONFIG_FILES([output:$file],, [file=$file])

automake will output rules to clean output, and
rebuild it. However the rebuild rule will not depend on input,
and this file will not be distributed either. (You must add
‘EXTRA_DIST = input’ to your Makefile.am if input is a
source file.)

will only cause input to be distributed. No file will be
cleaned automatically (add ‘DISTCLEANFILES = output out’
yourself), and no rebuild rule will be output.

Obviously automake cannot guess what value ‘$file’ is
going to hold later when configure is run, and it cannot use
the shell variable ‘$file’ in a Makefile. However, if you
make reference to ‘$file’ as ‘${file}’ (i.e., in a way
that is compatible with make’s syntax) and furthermore use
AC_SUBST to ensure that ‘${file}’ is meaningful in a
Makefile, then automake will be able to use
‘${file}’ to generate all of these rules. For instance, here is
how the Automake package itself generates versioned scripts for its
test suite:

Here cleaning, distributing, and rebuilding are done automatically,
because ‘${APIVERSION}’ is known at make-time.

Note that you should not use shell variables to declare
Makefile files for which automake must create
Makefile.in. Even AC_SUBST does not help here, because
automake needs to know the file name when it runs in order
to check whether Makefile.am exists. (In the very hairy case
that your setup requires such use of variables, you will have to tell
Automake which Makefile.ins to generate on the command-line.)

It is possible to let automake emit conditional rules for
AC_CONFIG_FILES with the help of AM_COND_IF
(see Optional).

To summarize:

Use literals for Makefiles, and for other files whenever possible.

Use ‘$file’ (or ‘${file}’ without ‘AC_SUBST([file])’)
for files that automake should ignore.

Use ‘${file}’ and ‘AC_SUBST([file])’ for files
that automake should not ignore.